General information for g1882.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g1882 is located on chr_3: 13641315..13642677 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g1882 | g1882.t4 | isoform | g1882.t4 | 13636538 | 13642677 |
| chr_3 | g1882 | g1882.t4 | TSS | g1882.t4 | 13636538 | 13636538 |
| chr_3 | g1882 | g1882.t4 | exon | g1882.t4.exon1 | 13636538 | 13636624 |
| chr_3 | g1882 | g1882.t4 | exon | g1882.t4.exon2 | 13641269 | 13641381 |
| chr_3 | g1882 | g1882.t4 | exon | g1882.t4.exon3 | 13641455 | 13641552 |
| chr_3 | g1882 | g1882.t4 | exon | g1882.t4.exon4 | 13641612 | 13641958 |
| chr_3 | g1882 | g1882.t4 | cds | g1882.t4.CDS1 | 13641886 | 13641958 |
| chr_3 | g1882 | g1882.t4 | exon | g1882.t4.exon5 | 13642223 | 13642677 |
| chr_3 | g1882 | g1882.t4 | cds | g1882.t4.CDS2 | 13642223 | 13642677 |
| chr_3 | g1882 | g1882.t4 | TTS | g1882.t4 | NA | NA |
Sequences
>g1882.t4 Gene=g1882 Length=1100
CAGTCGTTTCTCAACCGCGAGAGTGTGCAGATCGAAAAATCAAAATCTTTGCTTCTGCAC
GCACAACGTTTCATTAATACATTTTTTTTTGTGAGAATCTCTCCATGAATTTTCTATCAA
TACTCTAATAATTATGAATCACTCAGAAATATTATCATTTCTTCTACTACTATTTTGTGT
CTGTCAAAATTTCATTTCCGCATCACCACTTTTACCCTCCTCCTCATCATCAAATAATCG
TCGTCGAACGCGTTCGCAAATCGTAGCATGGAAACAGCCTGAAGATTATTGGAATATTAC
AAGCATTCCTAGAAGTATTTTACCTCATTTAATTAATAAAAATTTGAGCCATACGCTGCC
AGCACCAGCCAATATTATTTTTAAAACTGTCGATGCCGATGAAAAAATATTAGAGAGATT
TCATGAAATTAAGGTATGTTTAACTGATTAAAGCAAAAAATTAACGTTTAAAAATTTGTT
TCTATTAGAATAATATCACTGCAAGAACATTGTGGTCAAAAGCAGAAGCTGATCATCATT
ACTCGCCATTTTTCGATAAAGCACTGAAACTTATGAATCTCCAACAAGTCGCTTTTGAAA
TTGAAAACTCTGTGATGAGTAAAATGAGTTGTACAGCATGCAAAGCTGGAGCAACGCTAC
TTCAACATTATATAAAGTCTGGAAAGAGTAAAGAAGAAATCATTAAAACTATCTATCAAT
ACTGCACAAACCTACAAATTCAATCAGCTAGAGTTTGTGAAGGTGTCAGCAATCTCTTTG
GTGGTGAAGTTATTTACGTTCTCAAAAGAACAAACTTGGGTGCAGATGAGATTTGTAGTT
TTATAATTGGTGATGCATGCGGAGACATTTATAATCCTTATCATGAATGGGAAATTGAAT
TGCCTCCTGTACCAAAGCCACAACCTCATGAACTACCAATACCAAAAGAAAATGCACCAT
CATTTAAAGTTCTTCATTTGAGTGACACACATTTTGACCCTTATTATGAGGAAGGTAGTA
ATGCTGACTGTAATGAACCACTTTGCTGTAGAATAACTAATGGAAGACCAAGACATGTTA
ATGCGGCAGCTGGAAAGTAA
>g1882.t4 Gene=g1882 Length=175
MNLQQVAFEIENSVMSKMSCTACKAGATLLQHYIKSGKSKEEIIKTIYQYCTNLQIQSAR
VCEGVSNLFGGEVIYVLKRTNLGADEICSFIIGDACGDIYNPYHEWEIELPPVPKPQPHE
LPIPKENAPSFKVLHLSDTHFDPYYEEGSNADCNEPLCCRITNGRPRHVNAAAGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g1882.t4 | Gene3D | G3DSA:1.10.225.10 | Saposin | 13 | 98 | 0.0000000 |
| 2 | g1882.t4 | PANTHER | PTHR10340 | SPHINGOMYELIN PHOSPHODIESTERASE | 4 | 175 | 0.0000000 |
| 3 | g1882.t4 | PANTHER | PTHR10340:SF34 | SPHINGOMYELIN PHOSPHODIESTERASE | 4 | 175 | 0.0000000 |
| 1 | g1882.t4 | Pfam | PF05184 | Saposin-like type B, region 1 | 19 | 54 | 0.0000006 |
| 8 | g1882.t4 | ProSiteProfiles | PS50015 | Saposin B type domain profile. | 16 | 100 | 12.5910000 |
| 6 | g1882.t4 | SMART | SM00741 | sapb_4 | 18 | 96 | 0.0000000 |
| 5 | g1882.t4 | SUPERFAMILY | SSF47862 | Saposin | 17 | 99 | 0.0000000 |
| 4 | g1882.t4 | SUPERFAMILY | SSF56300 | Metallo-dependent phosphatases | 122 | 162 | 0.0000303 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006629 | lipid metabolic process | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
